potential energy of two body potential

Hello lammps users, I have a doubt, when I compute the potential energy
only of two particles when a two body potential, in this case I used
lj_cut, the energy of system is the half of energy that should be, in the
input file, I chose epsilon equal 1.0 and sigma equal 1.0, so in this case
for a distance between particles equal to 2^(1/6)*sigma = 1.2246 the
energy would be the equal to the well depth potential emin = 1.0.

# calculating potential energy

units lj
atom_style atomic
boundary p p p
lattice sc 1.0
region box1 block 0.0 10.0 0.0 10.0 0.0 10.0
create_box 1 box1
create_atoms 1 single 0.0 0.0 0.0
create_atoms 1 single 0.0 0.0 1.12246
mass 1 1.0

pair_style lj/cut 8.0
pair_coeff 1 1 1.0 1.0 8.0

neighbor 0.3 bin
neigh_modify every 1 delay 1 check yes
run_style verlet

fix 1 all nve
compute peratom all pe/atom pair
compute Pe all reduce sum c_peratom
thermo_style custom step temp ke pe etotal c_Pe
thermo 1
dump 4 all custom 1 particles.dat id x y z c_peratom
run 0

LAMMPS (1 Feb 2014)
# calculating potential energy

units lj
atom_style atomic
boundary p p p
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
region box1 block 0.0 10.0 0.0 10.0 0.0 10.0
create_box 1 box1
Created orthogonal box = (0 0 0) to (10 10 10)
  1 by 1 by 1 MPI processor grid
create_atoms 1 single 0.0 0.0 0.0
Created 1 atoms
create_atoms 1 single 0.0 0.0 1.12246
Created 1 atoms
mass 1 1.0

pair_style lj/cut 8.0
pair_coeff 1 1 1.0 1.0 8.0

neighbor 0.3 bin
neigh_modify every 1 delay 1 check yes
run_style verlet

fix 1 all nve
compute peratom all pe/atom pair
compute Pe all reduce sum c_peratom
thermo_style custom step temp ke pe etotal c_Pe
thermo 1
dump 4 all custom 1 particles.dat id x y z c_peratom
run 0
Memory usage per processor = 3.37525 Mbytes
Step Temp KinEng PotEng TotEng Pet
       0 0 0 -0.5 -0.5 -0.5
Loop time of 4.05312e-06 on 1 procs for 0 steps with 2 atoms

Pair time (\) = 0 \(0\) Neigh time \() = 0 (0)
Comm time (\) = 0 \(0\) Outpt time \() = 0 (0)
Other time (%) = 4.05312e-06 (100)

Nlocal: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14 ave 14 max 14 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1 ave 1 max 1 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1
Ave neighs/atom = 0.5
Neighbor list builds = 0
Dangerous builds = 0

I don't know why that happens, I try when another distance and the factor
2 appears always. Thanks I hope you help.

Samuel

From the units doc page, “Note that for LJ units, the default mode of thermodyamic output via the thermo_style command is to normalize energies by the number of atoms, i.e. energy/atom. This can be changed via the thermo_modify norm command.”.

Ray